diff --git a/NAMESPACE b/NAMESPACE index 0dd7970..ac43cde 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -17,7 +17,6 @@ export(impute.nuc_norm) export(impute.pca_bayes) export(impute.pca_prob) export(normalize) -export(preProcessFiltering) export(preprocessing) export(preprocessing_scaffold) export(pullProteinPath) diff --git a/R/filterings.R b/R/filterings.R index 4b77c03..99ccabb 100644 --- a/R/filterings.R +++ b/R/filterings.R @@ -49,7 +49,7 @@ #' #' @autoglobal #' -#' @export +#' @noRd preProcessFiltering <- function(dataSet, filterNaN = TRUE, diff --git a/R/preprocessing.R b/R/preprocessing.R index c5c53ec..50e7657 100644 --- a/R/preprocessing.R +++ b/R/preprocessing.R @@ -115,6 +115,8 @@ preprocessing <- function(fileName, ## select columns necessary for analysis selectedData <- filteredData %>% + mutate(R.Condition = as.character(R.Condition), + R.Replicate = as.character(R.Replicate)) %>% select(R.Condition, R.Replicate, PG.Quantity, PG.ProteinNames, PG.ProteinAccessions) ## print summary statistics for full raw data set diff --git a/R/visualizations.R b/R/visualizations.R index 7dbfd93..4a296f2 100644 --- a/R/visualizations.R +++ b/R/visualizations.R @@ -220,8 +220,7 @@ visualize <- function( } else if (graphType == "normalize") { plotData <- dataSet %>% - pivot_longer(-c(R.Condition, R.Replicate)) %>% - mutate(across(c(R.Condition, R.Replicate), as.character)) + pivot_longer(-c(R.Condition, R.Replicate)) ggplot(plotData, aes(x = R.Condition, y = value, fill = if (length(unique(R.Replicate)) == 1) R.Condition else R.Replicate)) + diff --git a/README.md b/README.md index 91598af..2dfe626 100644 --- a/README.md +++ b/README.md @@ -47,5 +47,5 @@ build this package. 2. `sh: /opt/gfortran/bin/gfortran: No such file or directory` The [GFortran](https://fortran-lang.org/learn/os_setup/install_gfortran/) compiler is -required to build this package. +required to build this package. diff --git a/docs/404.html b/docs/404.html index a39c06a..bfa63ef 100644 --- a/docs/404.html +++ b/docs/404.html @@ -8,65 +8,54 @@ Page not found (404) • msDiaLogue - - - + + + - Skip to contents - -